@eggbean, I turned off emails from the forum because I was getting a lot of spammers. Since then they've stopped posting, so I'll turn it back on.
To add/remove commands, edit your /root/.TRIGGERcmdData/commands.json file. Make sure you make them background commands because you're running the background agent.
The background agent adds, removes, and runs background commands.
FYI, if you find that your commands.json keeps reverting as soon as you save it, that means you've made some mistake in the json formatting so the agent restored the last good version of it.